GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Thiothrix lacustris DSM 21227

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::G3LHY8
         (358 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  161 bits (408), Expect = 2e-44
 Identities = 102/339 (30%), Positives = 167/339 (49%), Gaps = 9/339 (2%)

Query: 1   MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60
           +L L N +K   +   +   +L ++ G    +LGP+  GKT+++RL+AG ++P  G I  
Sbjct: 6   ILTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILL 65

Query: 61  DGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLK 120
           +G D+  +P +KR    V+Q +  +P LTV++N+A  ++++G D   I   V  A  +++
Sbjct: 66  NGDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVR 125

Query: 121 LTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQ 180
           L+ +  R P  LSGGQ+QR A+ARA+V    ++L+DE L+ LDYKLR++++ EL ++  Q
Sbjct: 126 LSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQ 185

Query: 181 SGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTL 240
            G  FVY T +  EAL +      ++ G+  Q G   E+Y  P NL  A    +  +N  
Sbjct: 186 LGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGE--INVF 243

Query: 241 D---VTKSGNVFTRPS--GVTIPVPSHLAVVPDGPVTIAFHPHHLGL--APQTGDAARLQ 293
           D   V   G      S  GV   +           V +   P  L +   P   +     
Sbjct: 244 DGEIVQALGEYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDLRIDCRPDVAERKGFP 303

Query: 294 ARTLVSEITGSESFVHLEYDGVRWVMLAHGIHDIDPDME 332
              L    TG     H+E +  + +M      + DPD +
Sbjct: 304 GIVLERSYTGQTLNSHIELENGQTLMAHEFFDEDDPDFD 342


Lambda     K      H
   0.319    0.136    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 276
Number of extensions: 13
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 369
Length adjustment: 29
Effective length of query: 329
Effective length of database: 340
Effective search space:   111860
Effective search space used:   111860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory